Human protein-coding genes and gene feature statistics in 2019
Abstract Objective A well-known limit of genome browsers is that the large amount of genome and gene data is not organized in the form of a searchable database, hampering full management of numerical data and free calculations. Due to the continuous increase of data deposited in genomic repositories...
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doaj-c1d93a9ee23f444a9b6554332c80364b2020-11-25T03:41:56ZengBMCBMC Research Notes1756-05002019-06-011211510.1186/s13104-019-4343-8Human protein-coding genes and gene feature statistics in 2019Allison Piovesan0Francesca Antonaros1Lorenza Vitale2Pierluigi Strippoli3Maria Chiara Pelleri4Maria Caracausi5Unit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of BolognaUnit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of BolognaUnit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of BolognaUnit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of BolognaUnit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of BolognaUnit of Histology, Embryology and Applied Biology, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of BolognaAbstract Objective A well-known limit of genome browsers is that the large amount of genome and gene data is not organized in the form of a searchable database, hampering full management of numerical data and free calculations. Due to the continuous increase of data deposited in genomic repositories, their content revision and analysis is recommended. Using GeneBase, a software with a graphical interface able to import and elaborate National Center for Biotechnology Information (NCBI) Gene database entries, we provide tabulated spreadsheets updated to 2019 about human nuclear protein-coding gene data set ready to be used for any type of analysis about genes, transcripts and gene organization. Results Comparison with previous reports reveals substantial change in the number of known nuclear protein-coding genes (now 19,116), the protein-coding non-redundant transcriptome space [now 59,281,518 base pair (bp), 10.1% increase], the number of exons (now 562,164, 36.2% increase) due to a relevant increase of the RNA isoforms recorded. Other parameters such as gene, exon or intron mean and extreme length appear to have reached a stability that is unlikely to be substantially modified by human genome data updates, at least regarding protein-coding genes. Finally, we confirm that there are no human introns shorter than 30 bp.http://link.springer.com/article/10.1186/s13104-019-4343-8Human genesProtein-coding genesGene statistics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Allison Piovesan Francesca Antonaros Lorenza Vitale Pierluigi Strippoli Maria Chiara Pelleri Maria Caracausi |
spellingShingle |
Allison Piovesan Francesca Antonaros Lorenza Vitale Pierluigi Strippoli Maria Chiara Pelleri Maria Caracausi Human protein-coding genes and gene feature statistics in 2019 BMC Research Notes Human genes Protein-coding genes Gene statistics |
author_facet |
Allison Piovesan Francesca Antonaros Lorenza Vitale Pierluigi Strippoli Maria Chiara Pelleri Maria Caracausi |
author_sort |
Allison Piovesan |
title |
Human protein-coding genes and gene feature statistics in 2019 |
title_short |
Human protein-coding genes and gene feature statistics in 2019 |
title_full |
Human protein-coding genes and gene feature statistics in 2019 |
title_fullStr |
Human protein-coding genes and gene feature statistics in 2019 |
title_full_unstemmed |
Human protein-coding genes and gene feature statistics in 2019 |
title_sort |
human protein-coding genes and gene feature statistics in 2019 |
publisher |
BMC |
series |
BMC Research Notes |
issn |
1756-0500 |
publishDate |
2019-06-01 |
description |
Abstract Objective A well-known limit of genome browsers is that the large amount of genome and gene data is not organized in the form of a searchable database, hampering full management of numerical data and free calculations. Due to the continuous increase of data deposited in genomic repositories, their content revision and analysis is recommended. Using GeneBase, a software with a graphical interface able to import and elaborate National Center for Biotechnology Information (NCBI) Gene database entries, we provide tabulated spreadsheets updated to 2019 about human nuclear protein-coding gene data set ready to be used for any type of analysis about genes, transcripts and gene organization. Results Comparison with previous reports reveals substantial change in the number of known nuclear protein-coding genes (now 19,116), the protein-coding non-redundant transcriptome space [now 59,281,518 base pair (bp), 10.1% increase], the number of exons (now 562,164, 36.2% increase) due to a relevant increase of the RNA isoforms recorded. Other parameters such as gene, exon or intron mean and extreme length appear to have reached a stability that is unlikely to be substantially modified by human genome data updates, at least regarding protein-coding genes. Finally, we confirm that there are no human introns shorter than 30 bp. |
topic |
Human genes Protein-coding genes Gene statistics |
url |
http://link.springer.com/article/10.1186/s13104-019-4343-8 |
work_keys_str_mv |
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